Active Setup: Batchfile is not adding registryfiles

I run a batchfile via active setup. This batch file is adding .reg-files to the HKCU of the user (folder view-settings, etc).
The batchfile does it's job when I run manually as an user. When it's been started by active setup, the registry keys are not applied. For debugging I added "echo 1 > %temp%\1.log", which showed that the batchfile was started and each command line (eg "regedit /s HKCU_Remove_recent_from_startmenu.reg) was started as well.
Anybody any ideas?

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Answers

I had some trouble with this on one of our installs. I ended up creating an exe using Autoit that ran the reg keys. For whatever reason I had better luck running an exe rather the a reg file. Not sure if it was just my enviroment or not.

@dugullett: Yes, 64Bit
@pjgeutjens: You'll see nothing of that at all, cause the batch runs before the desktop is ready. When you redirect the output to a file (eg
regedit /s HKCU_Remove_recent_from_startmenu.reg > %temp%\logfile.log), it'll be empty
@akki: this is my batch:

@FerrisBueller:
1. Have you given the proper path as in
"%alluserspath%\HKCU_Remove_recent_from_startmenu" in your batch file, i dont
see this in you batch file.
2. If possible give it a try through VBScript.